Naruto: Rise of cobra
by scouttroop
Summary: Abandon by his sensei, horribly scarred by Orochimaru and trained by Doctor Mindbender. Naruto returns to EN during the 4th war for revenge for the events in the valley of the end and the things of the past as the Doctor just before becoming Cobra commander. Rise of Cobra style.
1. Mindbender beginning

**Mindbender beginning **

**Hello everyone and here's another new story called Naruto: Rise of cobra. It's idea given to me by Haseo55. I hope you like it.**

**Disclaimers: I don't own Gi joe of Naruto, Hasbro and Masashi Kishimoto owns them.**

Valley of the end

Naruto and Sasuke lay where they are completely beaten, exhausted and battered. Before all this Sasuke was going to Orochimaru for power so he could get his revenge on Itachi. Sasuke was ignoring the fact that Orochimaru wants his sharingan, Naruto and his team went after him but they got cornered by the sound four. Shikamaru and the others manage to defeat them while Naruto deals with Sasuke.

"Kakashi sensei help me up", Naruto said after Kakashi arrived.

"I'm sorry Naruto but Sasuke needs more help than you", what Kakashi said made Naruto go wide eye.

Naruto then screams to his sensei as he picks Sasuke up and abandons him. Naruto still lying where he is unable to get up is now confronted by Orochimaru and Kabuto.

Orochimaru's lair one week later

Screams of pain can be heard from outside the lair, Naruto is being tortured by Orochimaru who is using a snake like whip.

"You terribly and horribly scarred him lord Orochimaru", Kabuto said with a smirk on his face.

"I know but even he escapes he will lived with those scars for the rest of his life", he said as he continue to torture him.

1 year later Naruto manage escape his captivity and leave the elemental nations.

"I can't go back to Konoha not after what Kakashi did, especially not on my condition."

As the boat sails out of the elemental nation Naruto blacks out because he had to drag his way to a boat and get it ready to sail.

5 days and 4 nights later Naruto finds himself in some kind of lab. He looks around and sees an old man in in a video player.

"**This will only hurt a little what comes next more so**", the old man ejects something into a man strap to chair.

Soon after the injection the man's skin and flesh starts to melt or get eaten away, Naruto looks at the things that were injected into the man.

"Nanomites", Naruto said while holding a sample of the Nanomite.

Naruto then sees the name of the old man, it's Doctor Mindbender.

"Magnificent isn't", Naruto turns around and sees Mindbender.

"I brought you here to see this when you recovered and I'm sure hoping you are interested on learning how to use my creation."

"Yes train me how to use them", Naruto said as Mindbender seals the door.

"I will tell you everything about the nanomites and I will give you the proper medical equipment so you can live onward", he explains to Naruto.

Dr Mindbender also gives Naruto a new ninja headband with a red cobra snake symbol on it. He even gives a mask a strange mask.

"When you're ready you can return to where you came from and start you're revenge on what they did to you."

Then a horrible laugh is heard from outside from the bunker. The one making that laugh was Naruto. It seems he is about become insane.

"Nanomites perfect little soldiers", Dr Mindbender said to Naruto.

**This chapter is finished. The story will go on like the film, Naruto will be the Doctor first before becoming Cobra commander. First he along with Storm shadow (same one from the film) will side with Obito/Madara Uchiha during the 4****th**** war, Cobra will not be there until the end. The GI JOES are not there but the shinobi alliances are the JOES. Cobra troopers are the same ones from the first film. Please review.**

**Next: Viper Commandos**


	2. Viper commandos

**Viper commandos**

**Here's the next chapter were the viper commandos make their appearance to the elemental nation.**

**Disclaimers: I own nothing**

The Elemental nation is at war again, it was now known as the fourth shinobi world war. The war was declared by Tobi/Obito Uchiha when the 5 kage and the leader of the land of iron refused to surrender the 8 tails and 9 tails for his eye of the moon plan. Tobi/Obito then stated that he will use the 7 tailed beasts that were capture by the Akatsuki years before to combat the ninja world. Soon after the start of the war the 5 great nations formed the shinobi alliance while Kabuto Yakushi formed alliance with Tobi, after a lot failed attempts to defeat the alliance like using the reincarnation, another ally joins up with Tobi.

In a forest far away from Konoha

Sasuke and Sakura and several other Konoha, Suna and Kumo nins (same number of soldiers in Duke and Ripcord's battalion) are on patrol. They are finished and now they are going to regroup with a recon team but they are about to get ambush and the recon team that they are supposed to meet up with isn't there.

"Excuse Sasuke was recon team that were supposed to meet here?"

"Yeah this is the spot and where are they?" Sasuke answered Sakura question.

"Eyes out", Sasuke asked the shinobi team if they see anything.

"Sweeps still clean sir", a random kumo nin said after checking his laptop.

"There is nothing here but us."

Then high above them a cobra gunship flies over them.

"What the hell is that?!"

The cobra gunship then fires it's pulse cannon killing 2 members. Then it fires again killing 2 more members. The battalion use fire jutsu to blow it out of the sky but the gunship is fireproof.

"Everybody get out of the way it's going to fire again!" Sasuke warns everyone.

The cobra gunship fires again which Sasuke and Sakura manage get out the way but some the others weren't so lucky.

"You all right Sakura?" Sasuke said helping her up.

"Yeah I am but my leg is pinned", Sakura said while Sasuke watches the cobra gunship landing.

The gunship lands then viper commandos steps out with Baroness. When the alliance spots them they carelessly charged at them only to be killed by the viper commando's pulse rifle which caused them fly back after being hit by them. Kunai and shurikens only bounces off their armor they just not hitting their weak spots or they are not using paper bombs. Baroness fires her pulse pistol at 2 shinobi nins coming at her then she turns around and spots someone she recognise when she zoom in her eye glasses.

"Where are going?" Sakura asked Sasuke after he put her down next to a tree.

"I have to help the others", Sasuke said as he runs to help the others.

Little does he know the viper commandos wiped out his entire company of nins.

"Don't move!" a viper commando said pointing his pulse rifle at Sasuke.

Baroness lowers his pulse rifle so she can't introduce herself to Sasuke, she press a button her eye glasses to make her eyes visible.

"Hello Sasuke", she greeted him.

"Mom?" after saying that, Mikoto/Baroness kicks him right in the face.

"Let you know you had that coming."

The moment gets interrupted when reinforcements arrives for Sasuke and Sakura. Yugao appears and knocks 2 viper commandos to the ground while Sasuke chased after Mikoto/Baroness after stabbing one viper commando in the eye. Yugao kills the 2 viper commados by throwing kunai knifes right through their helmet and into their eyes. One viper commando attempts to shoot Sasuke who is chasing after Mikoto/Baroness.

"Huh?" the viper commando looks up after being whistled. Then a kunai with a paper bomb hits the helmet and blows his head.

Tenten throws a kunai paper bomb at another viper commado at the armor, the viper commando falls down then gets up. Tenten throws another and the viper commando falls down again and gets up again. Tenten then takes cover as the viper commando fires causing her to fall down and throw her paper bomb kunai up in the air. Tenten crawls to reach her remaining paper bomb kunai but the viper commando steps on it.

"Bye bye", he pointing his pulse rifle at her.

It was cut short when he looks up and the paper bomb kunai lands on his helmet and blows his head off.

Back with Sasuke and Mikoto/Baroness

Sasuke is still chasing her and screaming her name or just calling her mom. The chase came to end when Sasuke grabs her by the waist but she kicks him off and she grabs a cable line from a cobra gunship. The gunship then leaves the scene, as for Sasuke he is very confuse because how is his mother alive and why is she against him. He then regroups with the others and heads back to konoha.

"I have a feeling those armored soldiers are the new allies of Tobi and Kabuto", Sasuke said.

"Yeah we know Sasuke and their only weak point blowing their head off or stabbing them in the eyes", Yugao said while she and Tenten are helping Sakura up.

What they don't know is that Naruto is the new ally of Tobi and Kabuto but they too have no idea their new ally is really Naruto. Naruto has his own agenda that's against Tobi, but as the doctor he will not use it now.

**The chapter is finished. Yugao will have the roll of Snake eyes like in my previous story, she will speak but never to Storm shadow. For the others they can be any of the JOES and you know Sasuke will be Duke. The Mikoto who is Baroness will have a revelation about her being alive. Please review**

**Next: The doctor **


	3. The doctor

**The doctor**

**Ok everybody here's another chapter were we meet the doctor who is actually Naruto by nobody knows that.**

**Disclaimers: I own nothing**

While on patrol and meeting we a recon team Sasuke, Sakura and their entire company of ninjas are suddenly ambush by a cobra gunship, after the gunship landed armored soldiers known as viper commandos emerged from it and they wiped out all of the ninja teams that were with Sasuke and Sakura. There was woman with them and she is Baroness but she was actually Mikoto Uchiha the mother of Sasuke Uchiha. Soon after reinforcements arrived and defeated all the viper commandos Mikoto/Baroness retreats leaving a very confused Sasuke behind.

With Obito/Tobi and Kabuto

A cobra submarine carrying Obito/Tobi and Kabuto is heading back to their new underwater base and they are being escorted by mantis attack craft.

"You know those viper commandos are not too bad after all even thou they all fell at the hands of those alliance ninjas", Obito said while watching the events in the forest.

"Well at least we known the good doctor is very good on what he do", Kabuto said and then he plays a song with his whistle (same one Zartan used in of in both films).

After docking they went to meet the doctor who was waiting for them in a room filled with recruits, personnel and viper elite troopers. The doctor wears a black suit, black pants and shoes. He even wears a strange mask with a small glass that covers his left eye and he has black spikey hair.

"The king cobra, magnificent creature nature's grim reaper unseen until it strikes its venom could kill a very large animal in a single bite", the doctor talks about the cobra inside a glass box.

"Very nice", Obito said.

"So far we created 20 neo vipers 19 stands before you", the doctors shows them.

"How's it working?"

"We injected the swarm nanomites into each subject, when they finally stop screaming brain scan shows a completed activities of the cortex", the doctor explain to Obito.

"Demonstrated doctor", Obito ordered.

The doctor hits a button which made a single neo viper moved to the box and then opens a small lid which his arm can fit in and the cobra bites him but doesn't feel any pain.

"They feel no pain, morality or disengaged, they don't feel regrets, no remorse. The nanomites joined together as a fighting mechanism, first blocking then expelling the cobra's venom."

Inside the fang wounds the nanomites blocks the venom and shoots it back out and the venom leaks out of the neo viper's wound.

"Completely brilliant", Obito said while the doctor moves the neo viper back to the group and shuts the lid.

"So you tell me is it working?" he asked Obito.

"Send a team to ran de vu with Storm shadow and the Baroness", Obito said with a smirk on his face under his mask.

"Considered it done the shinobi alliance won't know what hit them", the doctor said while he and Obito leave the room the base personal hands the neo viper's their armor, helmets and weapons.

"The 20th neo viper is already in hiding and awaiting your signal", the doctor said about the other neo viper.

"You done, you thrown the cable out in the yard", Obito said while they stop in place.

"Now if we sold one nanomite warhead into the black market I can continue all my research."

"I understand you're hunger knowledge doctor but not now. The missiles you made aimed at Konoha, Suna and Iwa, soon after I get what I want, you can have all the research you want."

The doctor stares at Obito who's waking away, he is planning something against Obito so he can get his revenge for the events in the valley of the end and the things in the past when he was in Konoha.

Meanwhile

Sasuke and other are showing the leaders the armor and weapons of viper commandos they encountered in the forest. Shizune is checking the body of a dead viper commando with other medic ninjas.

"What do have Shizune?" Tsunade asked her.

"Well lady Tsunade there is something in the viper commando's body", Shizune shows the monitor to Tsunade.

They don't know about the nanomites or what they do.

"That's a swarm right?"

"Yes it is Tsunade", Shizune answered.

"Can we get it off this viper commando's body?" Tsunade asked Shizune about removing the swarm of Nanomites.

"I don't know lady Tsunade", Shizune answered.

Outside

Cobra mole pods are drilling their way to Konoha for an attack even if the gates are closed.

**That's all for this chapter and hope you like it. In rise of cobra removing the nanomites from a victim is impossible to do since Anna/Baroness had to stay in the USS flag to have them removed. If you seen the film the 20th neo viper was hiding in the white house to upper hand the president. You readers can take a guess the 20th neo viper is hiding in the elemental nation. Please review**

**Next: Neo vipers**


	4. Neo vipers

**Neo vipers**

**I'm back here now and here's the next chapter in Naruto rise of cobra.**

**Disclaimers: I own nothing**

In the aftermath of the attack by the viper commandos, Obito/Tobi and Kabuto is returning to their new underwater base. When they got back they met up with the doctor who was responsible for the creation nanomites and the neo vipers, after a demonstration on how the nanomites work inside the neo vipers Obito/Tobi orders the team of neo vipers to join up with Storm shadow and Baroness. In Konoha cobra mole pods are drilling their way underneath the village.

Konoha hokage tower

A lone anbu is on guard duty when he starts hearing noises coming from the walls. Quickly he unsheathes his sword and getting ready to fight whoever is coming through the walls. Bad news was the lone anbu was killed when the mole pod burst through the wall causing him to fly back and hit the wall killing him. Storm shadow, Baroness and the neo vipers emerges. 2 konoha nins spots them and charges at them but Baroness shoots them with her pulse pistol making them fly up and land on metal barrels killing them both. Storm Shadow made his move by slashing his sword to the right killing a konoha nin who was hiding. While 2 neo vipers head up all the mole pods were destroyed when dozens of kunai with paper bombs hit them.

"Now that's youthful", Might Guy just did that.

Baroness knocks Guy out with another shot with her pulse pistol.

"Finish what you're doing then were leaving", Baroness orders the other 2 neo vipers.

"Were on it", the duo enters the hokage office and knocks out both Tsunade and Shizune with a single shot with their pulse rifles.

"Clear", the neo viper said as he and the other make their way back to Storm shadow and Baroness.

Storm shadow and Baroness are preparing to leave but gets cornered by Sasuke. Baroness slowly walks to him.

"Stop mom, stop right there."

"You can't attack me can you?" Mikoto said with a smile on her face.

"I will if I have to."

"Deep down your still the same little boy I gave birth to."

"Don't force this."

"We could have been…." Mikoto didn't finish the sentence when she got closer to Sasuke.

"Stop right there dammit", Sasuke warns her while he puts his kunai to her throat.

"Stop or I'll slit her throat", he warns Storm shadow who going to pull out his sword.

"Do it, you already killed me once by leaving this village", Mikoto tells him.

"Sasuke look out!" Sakura shouted at him when she spotted a neo viper was about open fire at Sasuke.

The neo viper then turns and fires at Sakura by she manage to avoid the blast wave by sliding. She then kills the neo viper with an armored piercing spear.

"Woaaaahhh!" the neo viper dies after being speared.

Other konoha ninjas join the fight but some were killed by the neo viper's pulse rifle.

"Mom stop", Sasuke said but moves out of the way from a neo viper that shoots a wagon knocking Sasuke to a floor.

Sakura pulls out senbon needles but gets knock out of her hands by Storm shadow, he kicks her back and was about to strike her down until Yugao saves her from being killed.

"Hello sis", Storm shadow greeted her.

Yugao then sees flashes in her head when she and Storm shadow were young. They were sparring, young Storm shadow is using a sword and young Yugao is using tonfa arm blades. The flash ends and Yugao clashes with Storm shadow.

Back with Might guy

Guy gets back up and then spots a neo viper that's on fire but doesn't feel a thing. The neo viper then attacks him.

"Eat this", Guy said when he put a paper bomb on one spot that the neo viper couldn't reach.

The neo viper tries to pull it out but too late it blows his head off.

Back with Yugao and Storm shadow

They continue their clash until Storm shadow jumps to higher ground and Yugao follows him while he cuts down 2 konoha ninjas.

With Mikoto

As Mikoto attempts to leave but gets rammed by her old friend Kushina Uzumaki, apparently after the war began Kushina returned because she tought Naruto was dead which was told by Danzo Shimura, soon after she returned Danzo was executed for his traitorous ways as for Kakashi he gets a bad beating for leaving Naruto behind.

Back with Sasuke

Sasuke gets up and watches a neo viper firing at various konoha shinobi.

"Hey genius", Sasuke gets the neo viper's attention and he blows the paper bombs on the floor making the neo viper fly up and land on electric cables.

Mikoto continues her fight with Kushina until she gains the upper hand with chain and tries to strangle her. Before Kushina puts on a camouflage suit and at first she was winning but Mikoto drenched her with water making the camouflage suit useless. Mikoto then let's go when she notice Storm shadow is heading for the cobra gunship. Sasuke throws all of kunai knifes at a neo viper until he runs out and knocks the neo viper into a spike.

"Bye Sasuke got a fly", Mikoto kicks Sasuke while holding on the cable of the gunship that pulls her and Storm shadow up.

Sasuke again just watches the gunship flies away.

**Well that's the end of this chapter, Kushina is still alive in this story because the fight between Baroness and Scarlett, I match them up with Mikoto and Kushina. Please review.**

**Next: Flashbacks and next move**


	5. Flashbacks and next move

**Flashbacks and next move**

**Here's the next chapter were things from past shows up and the enemy's next move.**

**Disclaimers: I own nothing**

In the last chapter Konoha was under attack but it was in the Hokage tower. Storm shadow, Baroness and the neo vipers are the attackers. During the battle many konoha ninjas were killed due to the neo viper's pulse rifles, Baroness's pulse pistol and Storm shadow ninja skills. Sasuke Uchiha himself refuses to attack Mikoto because of the relationship with his mother, for Yugao her relationship with Storm shadow took place when they both young. The konoha nins defeated all of the neo vipers but Storm shadow and Baroness got away and again Sasuke just watches the cobra gunship fly away.

Konoha hospital

"Lady hokage and Shizune are stable for now but they won't be up until 2 days", a medic ninja said while checking Sasuke's injuries.

Sasuke sadly thinks again about his sudden hesitation on attacking his mother. Later on he meets up with Yugao who sitting in a hospital chair.

"Hey Yugao sensei looks like were both seeing ghosts", Sasuke said which she only nodded to him.

"I know Sasuke", Yugao said to him.

Flashback during Yugao's young age

Yugao herself orphan and sneaks into a kitchen of the arashikage clan which she is not aware of. Yugao quickly grabs something to eat until young Storm shadow shows up.

"Thief", Storm shadow attacks her but Yugao seemed to be very skilled with her ninja fights.

The fight lasted for 4 hours until the leader of the clan known as the hard master showed up and halts the fight. The hard master then asked what's going on.

"She's stealing", Storm shadow said pointing his finger at Yugao.

The hard master knows that but he is fascinated with Yugao's ninja skills and decided to let her join the arashikage clan.

"What's your name little girl?" the hard master asked and Yugao smiles at him.

Flashback end

Yugao then removes her right anbu glove and looks at arashikage clan symbol tattoo on her wrist that confirms that she was a member of the clan.

Underwater base

Obito/Tobi is discussing about their next move in their war with the shinobi alliance.

"Baroness, Storm shadow the doctor has a weaponized nanomite warhead. I want you to test it in one particular place", Obito/Tobi said to them.

"As you wish Tobi", Storm shadow said spinning his shuriken.

Meanwhile

The doctor is getting Kabuto ready for his mission he's about to carry out. Obito/Tobi showed up to see all this.

"One more thing I'll control mooned brains thank you very much", Kabuto said after pulling and crushing the object that was supposed to control him.

"Let's do this", Kabuto said lying down.

The doctor does his thing by injecting a large swarm of nanomites into Kabuto's head with needles.

"Oh that was a bit nasty", Kabuto said after feeling those needles going into his head.

"You think so", the doctor said.

"Let's run some test, eye color, hair color, gender change, skin color and height change", while the doctor works Kabuto screams due the nanomites work inside him.

Back at Konoha

"Hey I think we found them", Anko said the team.

Timeskip

While heading for their destination Sasuke thinks back again about the day his mother died.

Flashback Uchiha clan massacre

Sasuke sees the dead bodies of his parents who were killed which was caused by his brother Itachi.

End of flashback

Sasuke remembers his vow to avenge his clan but he learned a lot of truths like the part Itachi was actually ordered to do it by corrupt officials and the part on learning that his clan are planning to rebel against the village. Now the part of his mother being alive just makes him wonder how.

**This chapter is finish, now I hope you readers can guess who Kabuto will be guises as in the final chapter. Please review**

**Next: Steel crusher chase **


	6. Steel crusher chase

**Steel crusher chase**

**Hello my fellow readers and here's the next chapter where the konoha nins chase the steel crusher hummer.**

**Disclaimers: I own nothing**

In the last chapter Sasuke and Yugao thought back about their past, Sasuke thought about the night his mother was killed along with the rest of his clan. Yugao thought about the time she was part of the Arashikage clan even about her relationship with Storm shadow. Meanwhile at the underwater base Obito told Baroness and Storm shadow to test one of the Doctor's new nanomite warheads on one particular place, after they left the doctor do some test on Kabuto for his mission.

The test site for the nanomite warhead is the long-time enemy of konoha, iwagakure. The steel crusher hummer smashes its way through the gates also it smashes houses and other objects in the streets.

"There it is Sasuke", Sakura said with their new delta-6 accelerator suit (same one from the movie).

"Ok Sakura lets hit it", Sasuke said as they begin to chase it.

For Sakura, first she trips and falls then she gets back up and joins the chase.

Yugao jumps on top of the steel crusher and hangs on to it so the others can track them.

"Alright you got it Yugao but whatever you do don't let go of that vehicle", Anko said while watching the tracker.

Kushina rides a motorcycle to help Sasuke, Sakura and Yugao. With Yugao the steel crusher hummer begins to turn left and right just to make Yugao lose her grip. Yugao suddenly lose her grip and let's go.

"Looks like she has given up", Baroness said.

"She never gives up", Storm shadow corrects her after noticing that Yugao is underneath the vehicle.

Back with Anko

"What kind of course their heading anyway?" Kurenai asked Anko.

"Maybe somewhere the swarm of nanomites can destroy", Anko and Kurenai then stares at the Tsuchikage tower and finally realize what the enemy is up too.

"Oh my kami there going to destroy the tower", Kurenai said with wide eyes.

"Everyone you have to stop the steel crusher!" Anko warns the others.

"Were working on it", Kushina said.

"I mean right now, they're going to unleash the swarm of nanomites on the Tsuchikage tower!"

Sasuke and Sakura then open fire at the steel crusher hummer with their gatling submachine gun. Kushina starts to ram the hummer.

"That red head is starting to piss me off!" Baroness said angrily.

The steel crusher then fires rear missiles which Sasuke and Sakura manage to dodge and as for Kushina she gets off her bike and regroups with the others. Yugao gets back to the roof and punches through the steel crusher when she puts on brass knuckles.

Timeskip

The chase came to an end the steel crusher flips over after colliding with a wagon. Baroness and Storm shadow then go on foot with Sasuke and Sakura going after them. Baroness is armed with an mp7 smg, Sasuke and Sakura sees her going up and they open fire but misses.

"Split up Sakura", Sasuke told Sakura.

"You got it Sasuke", Sakura goes after Baroness.

Sakura catches up to Baroness. She points her mp7 at Sakura but she manages to knock it out of her hands. Baroness then grabs a pan of hot sauce and drenched Sakura with it. While Sakura wipes the hot sauce off Baroness fires the swarm of nanomites at the Tsuchikage tower and the swarm starts to eat the tower. Baroness then boards the cobra gunship that came to pick her up, but before the gunship leave Sasuke jumps inside it and hits the kill switches and all the nanomites deactivates. Storm shadow then knocks Sasuke out. The Tsuchikage tower is still standing but most of it was eaten away.

"They got Sasuke everyone", Sakura said when the cobra gunship flies away.

"Will get him back", Anko said.

"What's that Sakura?" Kushina asked what's on her face.

"Baroness drenched me with hot sauce Kushina sensei", Sakura answered.

**That all of it, I don't remember some of the scenes from Paris because I don't watch that scene. I have the movie anyway. Please review**

**Next: Sasuke captured**


	7. Sasuke captured

**Sasuke captured**

**Hello again my fellow readers and here's the next chapter in the story. I hope you enjoy.**

**Disclaimers: I own nothing**

Last time Sasuke, Sakura, Yugao, Kushina, Anko and Kurenai went after Storm shadow and Baroness who were going to unleash the swarm of nanomites on the Tsuchikage tower. First they have to stop their vehicle known as the steel crusher hummer which was a success, then the chase is on foot. During the chase the swarm of nanomites was unleashed on the tower but Sasuke manage to hit the kill switch deactivating them but parts of the tower where eaten. Sasuke was then captured.

Cobra gunship on the way back to the underwater base, Sasuke and Mikoto just stared at each other. For Storm shadow, he thinks back on that fateful day the hard master was killed.

Flashback

Storm shadow and Yugao spared but Yugao won the fight and the hard master favors Yugao his best student. Storm shadow just glares at her.

Next morning

Yugao was training on her own until he heard a scream from the hard master. She rushes to the scene where she finds the hard master dead, killed by a sword stabbed through him.

"Hard master", Yugao holds him in her arms and then she turns to her right and sees Storm shadow running away.

'Storm shadow how could you', Yugao thought while Storm shadow looks at her one last time before leaving.

End of flashback

Storm shadow knows after that incident Yugao vows never to say a word to him again except to others.

Back at Konoha

"You think we can find them?" Sakura asked Anko.

"Well we can't tracked the gunship", Anko said.

Tsunade shows up tells them that they already know where the cobra gunship is heading and it's the snow country.

Above the underwater base

The cobra gunship lands and the group heads for the elevator that goes down the underwater base. For Sasuke he pushes a viper elite trooper and runs off.

"No don't shoot", Baroness tells the viper elite trooper who pointed his g36 assault rifle at Sasuke.

Storm shadow throws a single shuriken making Sasuke fall after being hit on the back.

"What was your plan run half a mile across the ice? Stupid Sasuke", Storm shadow said to him before the viper elites pick Sasuke up.

Timeskip

Obito is overseeing the nanomite missile ready for launch until Baroness and Storm shadow returns with Sasuke. Obito then taunts Sasuke by kissing Baroness/Mikoto, Sasuke anger by that sight he hits Obito in the face, then 2 viper elites whack Sasuke with their g36 rifles, at the same time Mikoto begins to see flashes in her head. Then they went to meet the doctor.

"Well who is this, another recruit?" the doctor asked Obito.

"I say a very unwilling one doctor", Obito answered.

"I'll prepare him for the procedure", at the same time the doctor glares at Sasuke because as Naruto he blames him for the state he is in.

Outside a giant submarine (same on from the movie) burst out to the surface and 2 snow mobiles emerges from it and heads for their destination. 2 viper elites are guarding.

"You picking up anything?"

"Negative there's nothing on the scanner", he said until the snow mobiles became visible.

"Hold up", the duo aim their g36 but where both killed by snow mobile's guns.

The team gets off their vehicles.

"Wow that's a night raven they actually built one", Kushina said on the sight of the night raven.

"Looks fast, Obito has some gadgets", Sakura said about the night raven.

At the operation room

Sasuke is strap to a bed, the doctor is about to inject the nanomites inside him.

"You want to know something Sasuke, before all this I was always beaten as an orphan boy and left to rot in the streets because they think I was a monster in human form, I survive all that thanks to people who care about me, what I wanted is to be a better ninja and be accepted by others", the doctor explains his life as Naruto.

"Who are you?" Sasuke asked who he is, the doctor walks up to him.

"That's another story you'll know another time", the doctor said as he prepares to experiment on Sasuke.

Back at the surface as the team are trying to find a way inside 3 nanomite missiles launched and heads for their targets. Yugao drives and fires a missile from the snow mobile destroying the first missile.

Underwater base

"We lost the kumo nanomite missile", guy in the radio said.

"Alert all defenses!" Obito ordered.

"She's here", Storm shadow runs off to face Yugao.

Mikoto continues to see flashes in her head about the times she spend with her son, the nanomite programing has been overridden so she is going to help Sasuke.

Operation room

"Now Sasuke you will know what it's like to be a monster", but before he can inject the nanomites Mikoto appears and smacks the doctor and shuts off the machine.

Sasuke and Mikoto embrace each other.

"Oh my kami", Sasuke said after seeing the cobra symbol on her left side.

Suddenly Mikoto falls on the floor like she was tazed.

"Security to the operation room", the doctor said.

Sakura flies the night raven to destroy the last 2 missiles while the others find a way inside. Elsewhere the Fire Daimyo hides in a bunker in his home but is unaware what's going to happen next.

"Those are laser Yugao", Anko warns Yugao.

"Anything that touches that will be fried", Kushina said.

"Handstand will do the trick", Yugao said.

Operation again

"I going to kill you doctor", Sasuke said when Obito and 2 neo vipers entered.

"Is she still alive?"

"For now at least", the doctor said.

"I thought we had complete control of her you said this couldn't happen", Obito said in a panic.

"I didn't know I never seen someone override the program", the doctor said to Obito.

"She did this for her son", Obito stared at Sasuke.

Back with Yugao

"Ok all you need to do is rewire…" before Anko can finish Yugao just stabs it.

"Or you can just stab it", Anko said.

"This is Kushina where in", she tells the others.

At the submarine shark attack subs deploy for battle and mantis attack sub from the underwater base are deployed.

"Wait for the shinobi alliance to break formation", a cobra eel trooper tells the others.

The underwater battle begins the shark attack sub fires missile at the base. At the same time the pulse cannon is ready to fire.

Back at the operation room

Sasuke killed the 2 neo vipers with Mikoto's pulse pistol after a missile struck the place.

"You think she loved you, imagine you're life with her", Obito taunts Sasuke again.

"You may have reincarnated my mom into a living person but she still cares about me", Sasuke taunts Obito.

"That's it she dies!" the doctor said preparing to hit a button.

"Don't do it doctor!"

Obito use a flamethrower but the flame shoots back at Obito burning him when Sasuke fired the pulse pistol. Sasuke picks up the remote while the doctor leaves the operation room. Sasuke shuts off the nanomites and Mikoto awakens again.

"I'm going to get you out of here", Sasuke said picking Mikoto up in a bridal style.

Obito cries out in pain after being burned.

"Get up you're coming with me", the doctor said picking Obito up.

Meanwhile Kushina, Anko and Yugao kills all of the underwater base personal and viper elite troopers. One more viper elite is about to open fire but Yugao kills him with a pistol. Kushina then close all the doors to prevent any other enemies from coming in. The pulse cannon fires at the submarine damaging it, Tsunade then orders the team to destroy the pulse cannon.

"Ok Yugao the pulse cannon is located right here", Kushina tells Yugao then she heads for the cannon.

Viper elite troopers ran past Yugao as she heads for the cannon, Storm shadow follows her.

**Ok so far so good that's the end of the chapter I hope you like it. The rest will come in the next chapter. Please review**

**Next: Final fight**


	8. Final fight

**Final fight**

**Ok my fellow readers 1 more chapter after this is done, I hope you enjoy it.**

**Disclaimers: I own nothing**

Last time after arriving at the underwater base Sasuke was going to be corrupted by the nanomites after the doctor injects them into him, but Mikoto who overridden the nanomites inside her because of the flashes in her head saves him. Meanwhile the shinobi alliance battles the cobra eel troopers with their shark attack subs as for the others inside the base they have to guide Sakura who is piloting the night raven to destroy the 2 remaining nanomite missiles and Yugao was tasked to destroy the pulse cannon. Sasuke is getting his mother out of the base and at the same time he's going after the doctor and Obito.

In the sky Sakura is trying to destroy the 2 remaining nanomite missiles.

"Ok now I'm on target", Sakura said.

"Alright you have destroyed it", Anko said to Sakura.

"If the nanomites hits the surface it's all over, they'll destroy the village", Kushina warns Sakura.

"Ah we have a problem, the fire controls are not in here", Sakura said because there's not even a button for the night raven's weapons.

"What do you mean not in there?" Anko asked a bit sarcastic.

"I mean I don't see them", Sakura answered.

"It must be voice command", Kushina tells Sakura.

Sakura said every word to fire the night raven's weapons but nothing happing. Kushina then says the language is different so she tells her to try it in Japanese and it worked.

"You did it Sakura you just saved Iwa."

"Just doing my job Anko sensei now guided me to Konoha."

Guys at the pulse cannon is retargeting the shinobi alliance submarine but Yugao burst him and killed the 2 guys with her shuriken that flew into their face and eyes. She then throws another at a neo viper in the eye of the helmet's visor then she spin kicks him making him fall out of the room, first he gets cut in half after touching the electric fields which cause the pulse cannon to shut off. Yugao attempts to shut it off completely but gets interrupted by Storm shadow. Yugao dodges 2 shurikens thrown by Storm shadow, she blocks the last one with her gauntlet then she throws it back at him but missed. Yugao and Storm shadow square off again while 2 guys attempt to bring the pulse cannon back online. Storm shadow rams Yugao off the room so she can't stop them.

"Now you die", Storm shadow said as he attacks.

Storm shadow had the upper hand after Yugao's swords get knocked out of her hands but she had arm blades

Meanwhile

The doctor and Obito are heading to the cobra submarine which they got back.

"Launched admittedly and head for the icepack", the doctor ordered the neo vipers.

"Yes sir", the neo viper duo obeyed.

The cobra submarine leaves the falling base. Sasuke puts Mikoto down for a while he fires the pulse pistol at the squad of neo vipers who are blocking their path.

"We're going after the doctor and Obito", Sasuke said to Mikoto as they board the last mantis attack sub.

"Hey Kushina it's Sasuke he seems fine."

"But what is he doing with her?"

The mantis attack sub leaves the dock and goes after the cobra sub as it leaves the hangar other mantis attack subs goes after them.

"Mom shoot them down", Sasuke tells her.

"I loved to", Mikoto mans the turrets.

Sasuke then calls Kushina and Anko and tells to get out of the base but they can't not until Sakura finished off the last missile.

Back at the sky Sakura fires at the missile but missed. With Sasuke and Mikoto they seemed to be having trouble trying to shake the other mantis attack craft.

"Man I can't shake these guys", Sasuke said.

"Sasuke I'm out of weapons", Mikoto warns him.

Sasuke selects other weapons that mantis attack craft have. They try lazer artillery weapons which destroy one enemy mantis attack craft.

Yugao still fighting Storm shadow, Yugao cuts some of his flesh with her arm blades making Storm shadow remove his mask and jacket.

"When hard master was killed, you made a vow to only say a word to others but never to me. Now you will die without a word to me", Storm shadow made his sword into a staff blade.

In the sky again Sakura is still trying to destroy the last missile but suddenly the missile just gone drone.

"The missile just gone drone", Sakura warns the others.

Timeskip

The drone missile is near Konoha and is about to hit the hokage tower. Sakura fires and destroys the drone missile but the night raven was drenched with the swarm of nanomites and begins to eat the aircraft. Sakura takes the night raven high up in the atmosphere.

"Ok Sakura eject now", Kushina tells her which she did and the night raven's signal is lost.

At first there was no response from Sakura but then she answered the she is ok and everybody cheered. Sakura landed in the water in Konoha which the konoha nins helps her up. Kushina and Anko begin their way back to the elevator.

With Yugao and Storm shadow

The fight drags on Yugao gets the upper hand when she gets the staff sword of Storm shadow then she stabs him right in the stomach. Storm shadow looks at Yugao one last time before falling into the icy water.

'I'm sorry Storm shadow", Yugao thought to herself.

Yugao then head back to the elevator where Anko and Kushina are waiting for her as the underwater base crumbles.

"Sir there's a hostile mantis craft", the neo viper said.

"Seal the door", the doctor ordered.

The door begins to seal Sasuke fires 2 torpedoes which only one manage the cobra sub's rotors.

"Wait for the targeting", the cobra eel said.

They fire but miss and the mantis craft crashed into the sealed door and the last one gets destroyed by Sasuke's mantis attack craft.

"There's got another way to the sub", Sasuke then takes a different route to go after the doctor and Obito.

**Just one more chapter to go then were done. Please review. Some of you know Storm shadow survived that's why he returned in retaliation.**

**Next: Rise of Cobra commander **


	9. Rise of Cobra commander

**Rise of Cobra commander**

**This is the final chapter of Naruto: rise of cobra, I hope you like it. In this chapter Naruto finally becomes Cobra commander.**

**Disclaimers: I own nothing**

On the last chapter the underwater base was falling but the shinobi alliance are trying to rescue Sasuke and destroyed the nanomite missiles. It was a success, as for Yugao she fought against Storm shadow and finally killed him, Sasuke and Mikoto went after the doctor and a burn out Obito Uchiha with stolen mantis attack sub.

In the cobra sub

"Now we finally have a moment to ourselves, I design something an especially for you Obito", the doctor pulls out a needle like gun.

"NO!" Obito tells him not to do it.

"This will only hurt a little what comes next more so", the doctor sticks the needle into his neck and injects more nanomites into him.

"Nanomites perfect little healers", while he changes Obito face becomes chrome and became living metal.

"My face became living chrome metal?!" Obito said after touching his new chrome face.

"Obito Uchiha is no more now you are Destro", the doctor said to him.

"What have you done to me?!" Obito attempts to attack him but was subdued by a hit of a button.

"The time has come for the cobra to rise up and reveal himself", he puts on his new mask and looks at Destro.

"You will call me commander!" Naruto declares himself.

On the right side of the sub a red cobra symbol is placed on it. The cobra sub stops in front of the mantis attack craft.

"This Sasuke Uchiha stand by and prepare to be boarded", Sasuke said on the radio.

"Sir", the neo viper called Cobra commander.

"You are relentless Sasuke I'll give that much but what's to stop me from blowing you out of the water?" Cobra commander said and asked.

"Self-preservation, I'm taking you in Cobra commander", apparently Sasuke overheard all that.

"Hah ha hah! You in what army?" he laughed and asked.

"My army", Sasuke said as the remaining shark attack subs and the submarine surrounds the cobra sub.

Prison elsewhere

"You know Sasuke this is only just begun", Cobra commander warns him from inside his prison cell.

"I'll be waiting for you", Sasuke said before sealing the cells.

Hospital

Shizune, Sakura and other medic ninjas are checking Mikoto out.

"It seems Cobra commander wouldn't allow anyone to remove the nanomites", Shizune said after checking her entire body.

After the checkup Mikoto spends some time with her son.

"You know Sasuke after all I did you still want to help me?"

"Hey that wasn't you that was Baroness. When you're finally done you'll be seeing a lot me", Mikoto then smiles and embrace her son hoping they will spend more time again when she is finally removed from the hospital.

Sasuke then reunites with the others to continue the war that still going on.

"Well I guess will continue the war that still go on", Sasuke said.

"We all in", Sakura said.

"Hey I just hope we can find Naruto as well", Sasuke said.

"I sure hope so", Kushina said.

What they don't know is Naruto was Cobra commander but they'll never know until Cobra commander decides to reveal himself in front of the entire elemental nations.

Elsewhere

The fire daimyo returns to his quarters after the nanomites missile where destroyed. When he sits down he whistles the same song that Kabuto used back at the cobra sub. It turns out that Cobra commander had Kabuto pose as the fire daimyo after injecting the nanomites and the 20th neo viper was also posing as the fire daimyo's guards to upper hand the real fire daimyo. Now Kabuto under the guise of the fire daimyo awaits Cobra commander's next order.

Will see you next time in retaliation

**Naruto: rise of cobra is finish, I thank Haseo55 for giving me this idea. I hope enjoyed it. Please review**


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